NTA has no such intelligence built into it. It reports the Netflow traffic that it sees on a per-device basis. So, if 3 different Netflow sources (ie: switches or routers) each see the same traffic traversing them, they will all report it. That's just it doing its job. The intelligence should come from whoever is interpreting the results to be smart enough to know that traffic from a given source would have to traverse the 3 switches to get to the router.
That being said, it will also depend on how the traffic flows between the switches and how the switches are configured and even possibly their capabilities. Early on it was common to mainly get Netflow out of Layer-3 interfaces, so if the traffic traversed through 3 switches all on the same Layer-2 VLAN segment, it might not get reported from those switches at all. I believe some switches need to be explicitly configured to show Layer-3 switched or Layer-2 data and some switches might not be giving up Layer-2 Netflow data at all. So, what info you will get can depend on the hardware you're using and how you have it configured.
And yes, it is a bit confusing!!
Alright Craig, thanks for the info!